Difference between revisions of "Sandbox"

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* '''Description:''' alpha-L-arabinofuranosidase <br/><br/>
+
* '''Description:''' endo-1,5-alpha-L-arabinosidase <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''abfA''
+
|''abnA''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || alpha-L-arabinofuranosidase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || endo-1,5-alpha-L-arabinosidase
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || arabinan degradation
 
|style="background:#ABCDEF;" align="center"|'''Function''' || arabinan degradation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56 kDa, 5.344  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34 kDa, 8.618  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1500 bp, 500 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 939 bp, 313 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cstA]]'', ''[[araQ]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[araA]]'', ''[[ysdC]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14832&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14841&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
 
|-
 
|-
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:abfA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:abnA_context.gif]]
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU28720
+
* '''Locus tag:''' BSU28810
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/araABDLMNPQ-abfA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/abnA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11900]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11901]
  
 
=== Additional information===
 
=== Additional information===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides (according to Swiss-Prot)  
+
* '''Catalyzed reaction/ biological activity:''' Endohydrolysis of (1->5)-alpha-arabinofuranosidic linkages in (1->5)-arabinans (according to Swiss-Prot)  
  
−
* '''Protein family:''' glycosyl hydrolase 51 family (according to Swiss-Prot)
+
* '''Protein family:''' glycosyl hydrolase 43 family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot)
+
* '''Localization:''' extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1QW8 1QW8] (complex with Ara-alpha-Xyl, Geobacillus stearothermophilus),  [http://www.rcsb.org/pdb/explore.do?structureId=1PZ3 1PZ3] (Geobacillus stearothermophilus)
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1UV4 1UV4]
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P94531 P94531]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P94522 P94522]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28720]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28810]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.2.1.55 3.2.1.55]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.2.1.99 3.2.1.99]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[araA]]-[[araB]]-[[araD]]-[[araL]]-[[araM]]-[[araN]]-[[araP]]-[[araQ]]-[[abfA]]''
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' repressed by glucose ([[CcpA]])
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:''' the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
<pubmed>12949161 9084180, </pubmed>
+
<pubmed>18957862, </pubmed>

Revision as of 08:52, 11 June 2009

  • Description: endo-1,5-alpha-L-arabinosidase

Gene name abnA
Synonyms
Essential no
Product endo-1,5-alpha-L-arabinosidase
Function arabinan degradation
MW, pI 34 kDa, 8.618
Gene length, protein length 939 bp, 313 aa
Immediate neighbours araA, ysdC
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
AbnA context.gif
This image was kindly provided by SubtiList





The gene

Basic information

  • Locus tag: BSU28810

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Endohydrolysis of (1->5)-alpha-arabinofuranosidic linkages in (1->5)-arabinans (according to Swiss-Prot)
  • Protein family: glycosyl hydrolase 43 family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: extracellular (signal peptide) PubMed

Database entries

  • KEGG entry: [3]

Additional information

Expression and regulation

  • Operon:
  • Regulation:
  • Regulatory mechanism:
  • Additional information: the mRNA is very stable (half-life > 15 min) PubMed

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

Birgit Voigt, Haike Antelmann, Dirk Albrecht, Armin Ehrenreich, Karl-Heinz Maurer, Stefan Evers, Gerhard Gottschalk, Jan Maarten van Dijl, Thomas Schweder, Michael Hecker
Cell physiology and protein secretion of Bacillus licheniformis compared to Bacillus subtilis.
J Mol Microbiol Biotechnol: 2009, 16(1-2);53-68
[PubMed:18957862] [WorldCat.org] [DOI] (I p)

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